Whale Shark Movement Analysis
Madelyne Zhang
2026-01-14
## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
## ✔ dplyr 1.1.4 ✔ readr 2.1.5
## ✔ forcats 1.0.0 ✔ stringr 1.5.1
## ✔ ggplot2 4.0.0 ✔ tibble 3.3.0
## ✔ lubridate 1.9.4 ✔ tidyr 1.3.1
## ✔ purrr 1.1.0
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag() masks stats::lag()
## ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors## Linking to GEOS 3.13.0, GDAL 3.8.5, PROJ 9.5.1; sf_use_s2() is TRUElibrary(patchwork)
#install.packages("remotes")
#install.packages(
# "aniMotum",
# repos = c(
# "https://cloud.r-project.org",
# "https://ianjonsen.r-universe.dev"
# ),
# dependencies = TRUE
#)
library(aniMotum)## Warning: package 'aniMotum' was built under R version 4.5.2##
## Attaching package: 'aniMotum'
##
## The following object is masked from 'package:purrr':
##
## map1 Data
## Rows: 12173 Columns: 6
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (2): lc, sat
## dbl (3): id, lat, lon
## dttm (1): date
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.## # A tibble: 60 × 2
## id n
## <dbl> <int>
## 1 108093 30
## 2 108096 4
## 3 108097 66
## 4 108106 2
## 5 108113 71
## 6 108114 2
## 7 112557 167
## 8 112560 18
## 9 112562 8
## 10 112563 23
## # ℹ 50 more rowssharks <- sharks %>%
mutate(
date = stringr::str_replace(date, "-\\s+", "-"),
date = ymd_hms(date)
)## Warning: There was 1 warning in `mutate()`.
## ℹ In argument: `date = ymd_hms(date)`.
## Caused by warning:
## ! 15 failed to parse.## # A tibble: 60 × 2
## id n
## <dbl> <int>
## 1 164969 1655
## 2 203645 894
## 3 184025 833
## 4 220364 687
## 5 172246 546
## 6 172241 541
## 7 203646 537
## 8 172239 514
## 9 157790 505
## 10 175950 485
## # ℹ 50 more rows## # A tibble: 7 × 2
## lc n
## <chr> <int>
## 1 0 458
## 2 1 1216
## 3 2 2378
## 4 3 3825
## 5 A 788
## 6 B 3489
## 7 Z 19sharks <- sharks %>%
arrange(id,date)
sharks <- sharks %>%
filter(!is.na(date))
# Largest time gap data check
sharks %>%
filter (id == "172246")## # A tibble: 544 × 6
## id lat lon date lc sat
## <dbl> <dbl> <dbl> <dttm> <chr> <chr>
## 1 172246 1.63 -92.3 2017-09-27 16:44:00 2 UT
## 2 172246 1.65 -92.3 2017-09-28 01:25:00 B UT
## 3 172246 1.65 -92.3 2017-09-28 02:50:00 B UT
## 4 172246 1.56 -92.4 2017-09-28 14:08:00 B UT
## 5 172246 1.50 -92.5 2017-09-28 15:33:00 B UT
## 6 172246 1.58 -92.6 2017-09-28 16:17:00 3 UT
## 7 172246 1.57 -92.6 2017-09-28 17:06:00 2 UT
## 8 172246 1.49 -92.9 2017-09-29 12:43:00 B UT
## 9 172246 1.48 -92.9 2017-09-29 13:25:00 B UT
## 10 172246 1.47 -93.0 2017-09-29 16:06:00 2 UT
## # ℹ 534 more rows## # A tibble: 503 × 6
## id lat lon date lc sat
## <dbl> <dbl> <dbl> <dttm> <chr> <chr>
## 1 157790 1.40 -99.5 2017-07-18 13:02:00 2 UT
## 2 157790 1.40 -99.5 2017-07-18 13:04:00 2 UT
## 3 157790 1.40 -99.5 2017-07-18 13:08:00 2 UT
## 4 157790 1.40 -99.5 2017-07-18 14:42:00 B UT
## 5 157790 0.915 -101. 2017-07-20 17:11:00 0 UT
## 6 157790 0.916 -101. 2017-07-20 17:59:00 B UT
## 7 157790 0.774 -101. 2017-07-21 17:34:00 1 UT
## 8 157790 0.654 -102. 2017-07-22 16:32:00 B UT
## 9 157790 0.623 -103. 2017-07-23 15:26:00 A UT
## 10 157790 0.623 -103. 2017-07-23 16:07:00 A UT
## # ℹ 493 more rows## # A tibble: 26 × 6
## id lat lon date lc sat
## <dbl> <dbl> <dbl> <dttm> <chr> <chr>
## 1 203637 47.6 -122. 2020-06-12 23:55:28 1 NP
## 2 203637 47.6 -122. 2020-06-13 00:33:58 B NK
## 3 203637 47.7 -122. 2020-06-13 01:35:58 3 NP
## 4 203637 47.7 -122. 2020-06-13 01:42:58 B MA
## 5 203637 47.7 -122. 2020-06-13 01:50:58 2 SR
## 6 203637 47.7 -122. 2020-06-13 02:12:37 2 NK
## 7 203637 47.7 -122. 2020-06-13 03:11:28 2 NN
## 8 203637 47.7 -122. 2020-06-13 03:16:58 2 NP
## 9 203637 47.7 -122. 2020-06-13 03:20:28 3 MA
## 10 203637 47.7 -122. 2020-06-13 03:32:58 3 SR
## # ℹ 16 more rows## # A tibble: 15 × 6
## id lat lon date lc sat
## <dbl> <dbl> <dbl> <dttm> <chr> <chr>
## 1 203638 47.7 -122. 2020-06-12 23:55:08 2 NP
## 2 203638 47.7 -122. 2020-06-13 00:37:38 0 NK
## 3 203638 47.7 -122. 2020-06-13 01:36:08 3 NP
## 4 203638 47.7 -122. 2020-06-13 01:43:53 1 MA
## 5 203638 47.7 -122. 2020-06-13 01:52:08 3 SR
## 6 203638 47.7 -122. 2020-06-13 02:13:08 3 NK
## 7 203638 47.7 -122. 2020-06-13 03:11:08 2 NN
## 8 203638 47.7 -122. 2020-06-13 03:18:08 2 NP
## 9 203638 47.7 -122. 2020-06-13 03:20:08 3 MA
## 10 203638 47.7 -122. 2020-06-13 03:32:38 3 SR
## 11 203638 47.7 -122. 2020-06-13 03:45:08 3 MC
## 12 203638 47.7 -122. 2020-06-13 03:51:08 3 NK
## 13 203638 43.8 -123. 2020-06-14 01:25:45 Z SR
## 14 203638 -0.740 -90.3 2020-08-11 15:50:07 3 MC
## 15 203638 -0.741 -90.3 2020-08-11 15:55:11 3 NN## # A tibble: 19 × 6
## id lat lon date lc sat
## <dbl> <dbl> <dbl> <dttm> <chr> <chr>
## 1 203639 47.7 -122. 2020-06-12 23:54:24 2 NP
## 2 203639 47.7 -122. 2020-06-13 00:34:54 0 NK
## 3 203639 47.7 -122. 2020-06-13 01:36:24 2 NP
## 4 203639 47.7 -122. 2020-06-13 01:42:54 B MA
## 5 203639 47.7 -122. 2020-06-13 01:52:24 3 SR
## 6 203639 47.7 -122. 2020-06-13 02:13:04 3 NK
## 7 203639 47.7 -122. 2020-06-13 03:12:24 3 NN
## 8 203639 47.7 -122. 2020-06-13 03:16:54 3 NP
## 9 203639 47.7 -122. 2020-06-13 03:20:44 3 MA
## 10 203639 47.7 -122. 2020-06-13 03:32:54 3 SR
## 11 203639 47.7 -122. 2020-06-13 03:45:24 3 MC
## 12 203639 47.7 -122. 2020-06-13 03:52:39 3 NK
## 13 203639 -0.738 -90.3 2020-08-11 15:50:17 3 MC
## 14 203639 -0.739 -90.3 2020-08-11 15:55:32 3 NN
## 15 203639 1.63 -92.0 2020-08-17 14:03:43 0 NK
## 16 203639 1.64 -92.0 2020-08-17 14:35:48 1 NN
## 17 203639 1.64 -92.0 2020-08-17 14:36:03 B MB
## 18 203639 1.64 -92.0 2020-08-17 15:02:35 1 MA
## 19 203639 1.65 -92.0 2020-08-17 15:34:10 1 MC## # A tibble: 17 × 6
## id lat lon date lc sat
## <dbl> <dbl> <dbl> <dttm> <chr> <chr>
## 1 203644 47.7 -122. 2020-06-12 23:54:50 2 NP
## 2 203644 47.7 -122. 2020-06-13 00:38:20 0 NK
## 3 203644 47.7 -122. 2020-06-13 01:35:50 3 NP
## 4 203644 47.7 -122. 2020-06-13 01:43:50 0 MA
## 5 203644 47.7 -122. 2020-06-13 01:51:20 3 SR
## 6 203644 47.7 -122. 2020-06-13 02:12:29 3 NK
## 7 203644 47.7 -122. 2020-06-13 03:11:20 3 NN
## 8 203644 47.7 -122. 2020-06-13 03:16:20 3 MA
## 9 203644 47.7 -122. 2020-06-13 03:16:50 3 NP
## 10 203644 47.7 -122. 2020-06-13 03:32:50 3 SR
## 11 203644 47.7 -122. 2020-06-13 03:45:20 3 MC
## 12 203644 47.7 -122. 2020-06-13 03:52:00 3 NK
## 13 203644 -0.738 -90.3 2020-08-11 15:50:23 3 MC
## 14 203644 -0.741 -90.3 2020-08-11 15:55:25 3 NN
## 15 203644 1.33 -91.3 2020-08-19 16:02:09 0 NN
## 16 203644 1.39 -91.8 2020-08-19 16:03:18 0 MA
## 17 203644 1.39 -91.8 2020-08-19 16:24:40 B MC## # A tibble: 537 × 6
## id lat lon date lc sat
## <dbl> <dbl> <dbl> <dttm> <chr> <chr>
## 1 203646 47.7 -122. 2019-09-08 14:00:00 2 SR
## 2 203646 47.7 -122. 2019-09-08 15:17:00 3 NP
## 3 203646 47.7 -122. 2019-09-08 15:28:00 3 NK
## 4 203646 47.7 -122. 2019-09-08 15:37:00 2 SR
## 5 203646 47.7 -122. 2019-09-08 15:45:00 3 NN
## 6 203646 47.7 -122. 2019-09-08 17:08:00 2 NK
## 7 203646 47.7 -122. 2019-09-08 17:10:00 3 MA
## 8 203646 47.7 -122. 2019-09-08 17:25:00 2 NN
## 9 203646 47.7 -122. 2019-09-08 17:44:00 2 MC
## 10 203646 -0.738 -90.3 2020-08-11 15:49:30 3 MC
## # ℹ 527 more rows# Split for individuals with large temporal gaps - 172246 and 157790
# Also with 5 sharks that have huge movement that is "across the continent" after the MPM interpolation, which doesn't make sense biologically, so I headed back here at first to split these 5 sharks observations in advance.
split_table <- tibble(
id = c(
"172246",
"157790",
"203637",
"203638",
"203639",
"203644",
"203646"
),
split_time = ymd_hms(c(
"2017-09-30 16:21:00",
"2018-03-28 22:30:00",
"2020-06-13 03:50:58",
"2020-06-14 01:25:45",
"2020-06-13 03:52:39",
"2020-06-13 03:52:00",
"2019-09-08 17:44:00"
))
)2 EDA
2.1 Observation time gap between sharks
# Compute time gaps between consecutive observations within each individual
sharks_dt <- sharks %>%
arrange(id, date) %>%
group_by(id) %>%
mutate(
dt_hours = as.numeric(difftime(date, lag(date), units = "hours"))
) %>%
ungroup()
# Time gap statistics per individual
sharks_dt %>%
group_by(id) %>%
summarise(
n_obs = n(),
mean_dt = mean(dt_hours, na.rm = TRUE),
median_dt = median(dt_hours, na.rm = TRUE),
max_dt = max(dt_hours, na.rm = TRUE)
) %>%
arrange(desc(max_dt))## Warning: There were 3 warnings in `summarise()`.
## The first warning was:
## ℹ In argument: `max_dt = max(dt_hours, na.rm = TRUE)`.
## ℹ In group 16: `id = 131988`.
## Caused by warning in `max()`:
## ! no non-missing arguments to max; returning -Inf
## ℹ Run `dplyr::last_dplyr_warnings()` to see the 2 remaining warnings.## # A tibble: 60 × 5
## id n_obs mean_dt median_dt max_dt
## <dbl> <int> <dbl> <dbl> <dbl>
## 1 172246 544 49.0 0.788 25638.
## 2 157790 503 56.2 1.43 15434.
## 3 203646 537 16.4 0.456 8110.
## 4 112557 167 42.0 1.30 6018.
## 5 139119 5 853. 215. 2984.
## 6 175953 440 7.55 0.601 2314.
## 7 172241 541 4.60 0.806 1818.
## 8 139127 12 260. 22.1 1747.
## 9 139121 7 319. 68.6 1458.
## 10 203637 26 63.1 0.642 1428.
## # ℹ 50 more rowssharks_dt %>%
summarise(
min_hours = min(dt_hours, na.rm = TRUE),
q1_hours = quantile(dt_hours, 0.25, na.rm = TRUE),
median_hours = median(dt_hours, na.rm = TRUE),
mean_hours = mean(dt_hours, na.rm = TRUE),
q3_hours = quantile(dt_hours, 0.75, na.rm = TRUE),
max_hours = max(dt_hours, na.rm = TRUE)
)## # A tibble: 1 × 6
## min_hours q1_hours median_hours mean_hours q3_hours max_hours
## <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 0 0.365 0.773 12.2 1.68 25638.The median of the consecutive time gap is 0.73 hours, but the maximum gap is around 2.9 years, where the tracking window has a huge gap. Raw Argos telemetry exhibited highly irregular temporal sampling, with frequent short-interval transmissions interspersed with multi-month to multi-year gaps.
# Time gap histogram
ggplot(sharks_dt, aes(x = dt_hours)) +
geom_histogram(bins = 60) +
scale_x_log10() +
theme_bw() +
labs(
x = "Time gap between observations (hours, log scale)",
y = "Count"
)## Warning in scale_x_log10(): log-10 transformation introduced infinite values.## Warning: Removed 61 rows containing non-finite outside the scale range
## (`stat_bin()`).
sharks <- sharks %>%
mutate(id = as.character(id))
sharks <- sharks %>%
left_join(split_table, by = "id") %>%
mutate(
id = case_when(
is.na(split_time) ~ id,
date <= split_time ~ paste0(id, "_a"),
date > split_time ~ paste0(id, "_b")
)
) %>%
select(-split_time)
sharks %>%
count(id)## # A tibble: 67 × 2
## id n
## <chr> <int>
## 1 108093 30
## 2 108096 4
## 3 108097 66
## 4 108106 2
## 5 108113 71
## 6 108114 2
## 7 112557 167
## 8 112560 18
## 9 112562 8
## 10 112563 23
## # ℹ 57 more rowsInitially, the raw df contains 60 sharks, but since two of them have long time gap which caused non-convergence in the first attempt of MPM, and 5 of the sharks’ movement track contains the “over-continent” track, which doesn’t make sense biologically, so these sharks are split into _a and _b to make further analysis. Therefore, with 7 sharks split to _a and _b, 67 sharks are remained.
# Raw Spatial tracks for each individual(points)
ggplot(sharks, aes(x = lon, y = lat)) +
geom_point(alpha = 0.4) +
facet_wrap(~id) +
theme_bw()
# Raw Spatial tracks for each individual(path)
ggplot(sharks, aes(x = lon, y = lat)) +
geom_path(alpha = 0.4) +
facet_wrap(~id) +
theme_bw()## `geom_path()`: Each group consists of only one observation.
## ℹ Do you need to adjust the group aesthetic?
## `geom_path()`: Each group consists of only one observation.
## ℹ Do you need to adjust the group aesthetic?
## `geom_path()`: Each group consists of only one observation.
## ℹ Do you need to adjust the group aesthetic?
# Check for id = 203637
# Geom_point
p1 <- ggplot() +
theme_bw() +
geom_point(
data = sharks %>% dplyr::filter(id == "203637_a"),
aes(x = lon, y = lat)
)
print(p1)
# Geom_path
p2 <- ggplot() +
theme_bw() +
geom_path(
data = sharks %>% dplyr::filter(id == "203637_a"),
aes(x = lon, y = lat)
)
print(p2)
2.2 Velocity check
# Stepwise speed between consecutive observations
sharks_speed <- sharks_dt %>%
mutate(
dist_m = geosphere::distHaversine(
cbind(lon, lat),
cbind(lag(lon), lag(lat))
),
speed_ms = dist_m / (dt_hours * 3600)
)ggplot(sharks_speed, aes(x = speed_ms)) +
geom_histogram(bins = 60) +
scale_x_log10() +
theme_bw() +
labs(x = "Raw speed (m/s, log scale)")## Warning in scale_x_log10(): log-10 transformation introduced infinite values.## Warning: Removed 63 rows containing non-finite outside the scale range
## (`stat_bin()`).
# proportion of raw steps exceeding 2.7m/s
sharks_speed %>%
summarise(
prop_over_2_7 = mean(speed_ms > 2.7, na.rm = TRUE)
)## # A tibble: 1 × 1
## prop_over_2_7
## <dbl>
## 1 0.123Approximately 12% of observed movement steps exceeded a biologically informed maximum swimming speed of 2.7 m/s.
2.3 Sanity check
Since the SSM model needs at least 3 points to fit, there are 9 sharks with less than 3 observations, which will be excluded from our further analysis.
## # A tibble: 9 × 2
## id n
## <chr> <int>
## 1 108106 2
## 2 108114 2
## 3 131988 1
## 4 132070 2
## 5 132073 2
## 6 139120 1
## 7 139122 1
## 8 203638_b 2
## 9 220357 2## # A tibble: 58 × 2
## id n
## <chr> <int>
## 1 108093 30
## 2 108096 4
## 3 108097 66
## 4 108113 71
## 5 112557 167
## 6 112560 18
## 7 112562 8
## 8 112563 23
## 9 120701 211
## 10 120702 46
## # ℹ 48 more rows58 sharks remaining in the sharks_ssm dataframe.
# Sanity check
# whether date contains invalid data
sharks_ssm %>%
summarise(
n_na_date = sum(is.na(date)),
n_inf_date = sum(!is.finite(as.numeric(date)))
)## # A tibble: 1 × 2
## n_na_date n_inf_date
## <int> <int>
## 1 0 0# Check whether lon / lat contains invalid data
sharks_ssm %>%
summarise(
n_na_lon = sum(is.na(lon)),
n_na_lat = sum(is.na(lat))
)## # A tibble: 1 × 2
## n_na_lon n_na_lat
## <int> <int>
## 1 0 0# Check whether time is monotonically increasing
sharks_ssm %>%
group_by(id) %>%
summarise(
any_non_increasing_time = any(diff(date) <= 0, na.rm = TRUE)
) %>%
filter(any_non_increasing_time)## # A tibble: 1 × 2
## id any_non_increasing_time
## <chr> <lgl>
## 1 203645 TRUEFor the sharks that have >= 3 observations, there are 0 observations of NA date as they were initially filted out. There are also non_increasing_time observations, which will be excluded.
# Check problem ids observations
problem_ids <- sharks_ssm %>%
group_by(id) %>%
summarise(any_non_increasing_time = any(diff(date) <= 0, na.rm = TRUE)) %>%
filter(any_non_increasing_time) %>%
pull(id)# Duplicated rows
sharks_ssm %>%
filter(id %in% problem_ids) %>%
count(id, date) %>%
filter(n > 1) %>%
arrange(desc(n))## # A tibble: 1 × 3
## id date n
## <chr> <dttm> <int>
## 1 203645 2020-09-16 04:23:41 21 duplicated entries found, will be removed.
2.4 Cleaning dataset for the SSM
# Final cleaned dataset used for state-space modelling
sharks_ssm_clean <- sharks %>%
# remove rows with invalid time or coordinates
filter(
!is.na(date),
is.finite(as.numeric(date)),
!is.na(lon),
!is.na(lat)
) %>%
# order observations within each individual
arrange(id, date) %>%
# remove duplicated timestamps within individuals
distinct(id, date, .keep_all = TRUE) %>%
# ensure each individual has enough data and strictly increasing time
group_by(id) %>%
filter(
n() >= 3,
all(diff(date) > 0)
) %>%
ungroup()In sharks_ssm_clean, all 58 sharks have at least three valid observations with valid timestamps and locations.
## [1] 12158## [1] 12142## [1] 67## [1] 58sharks_ssm_clean %>%
group_by(id) %>%
summarise(any_bad_time = any(diff(date) <= 0)) %>%
filter(any_bad_time)## # A tibble: 0 × 2
## # ℹ 2 variables: id <chr>, any_bad_time <lgl>There are 58 sharks (12142 entries) remaining.
3 SSM Model Fit
# State-space model settings:
# - model: correlated random walk (crw)
# - time.step: 24 hours (daily regularization)
# - vmax: 2.7 m/s (biologically informed maximum swimming speed)
sharks_crw_ssm <- fit_ssm(
x = sharks_ssm_clean,
model = "crw",
time.step = 24,
vmax = 2.7,
control = ssm_control(
verbose = 0
)
)## Warning in pf_sda_filter(x, spdf, vmax, ang, distlim):
## trip::sda produced an error on id 132071 using trip::speedfilter instead## Warning in pf_sda_filter(x, spdf, vmax, ang, distlim):
## trip::sda produced an error on id 139123 using trip::speedfilter instead## Warning in sqrt(as.numeric(object$diag.cov.random)): NaNs produced## Warning in sqrt(as.numeric(object$diag.cov.random)): NaNs produced## Warning in sqrt(as.numeric(object$diag.cov.random)): NaNs produced# Extract fitted locations (at observation times)
sharks_fitted <- grab(sharks_crw_ssm, what = "fitted") %>%
as_tibble()
# Extract predicted locations (regular 24 h interval)
sharks_predicted <- grab(sharks_crw_ssm, what = "predicted") %>%
as_tibble()## # A tibble: 58 × 5
## id ssm converged pdHess pmodel
## <chr> <named list> <lgl> <lgl> <chr>
## 1 108093 <ssm [15]> TRUE TRUE crw
## 2 108096 <ssm [15]> TRUE TRUE crw
## 3 108097 <ssm [15]> TRUE TRUE crw
## 4 108113 <ssm [15]> TRUE TRUE crw
## 5 112557 <ssm [15]> TRUE TRUE crw
## 6 112560 <ssm [15]> TRUE TRUE crw
## 7 112562 <ssm [15]> TRUE TRUE crw
## 8 112563 <ssm [15]> TRUE TRUE crw
## 9 120701 <ssm [15]> TRUE TRUE crw
## 10 120702 <ssm [15]> TRUE TRUE crw
## # ℹ 48 more rows# Identify individuals with non-converged SSM fits
nonconv_ids <- sharks_crw_ssm %>%
filter(!converged | !pdHess) %>%
pull(id)
nonconv_ids## [1] "172246_b"One individuals (“172246_b”) did not converge.
# Inspect observation histories of non-converged individuals
sharks_ssm_clean %>%
filter(id == "172246_b")## # A tibble: 529 × 6
## id lat lon date lc sat
## <chr> <dbl> <dbl> <dttm> <chr> <chr>
## 1 172246_b -1.14 -91.5 2017-10-08 17:02:08 1 MA
## 2 172246_b -1.11 -91.6 2017-10-08 20:13:45 1 NP
## 3 172246_b -1.11 -91.6 2017-10-08 21:49:35 3 NP
## 4 172246_b -1.10 -91.6 2017-10-08 22:58:34 3 SR
## 5 172246_b -1.10 -91.6 2017-10-08 23:18:30 2 NK
## 6 172246_b -1.09 -91.7 2017-10-09 00:35:55 3 SR
## 7 172246_b -1.09 -91.7 2017-10-09 00:54:48 3 NK
## 8 172246_b -1.09 -91.7 2017-10-09 01:01:39 3 NN
## 9 172246_b -1.08 -91.7 2017-10-09 02:24:28 3 MA
## 10 172246_b -1.08 -91.7 2017-10-09 02:38:31 3 NN
## # ℹ 519 more rows2017 jumped to 2020, which is probably the reason of non-convergence.
# Retain SSM fits that converged with a positive-definite Hessian
ssm_valid <- sharks_crw_ssm %>%
filter(converged, pdHess)
# Record IDs excluded due to non-convergence
ssm_excluded_ids <- sharks_crw_ssm %>%
filter(!converged | !pdHess) %>%
pull(id)
ssm_excluded_ids## [1] "172246_b"After excluding non-converged fits, 57 sharks remained for further analysis.
# Extract fitted and predicted locations from valid SSM fits only
sharks_fitted <- grab(ssm_valid, what = "fitted") %>%
as_tibble()
sharks_predicted <- grab(ssm_valid, what = "predicted") %>%
as_tibble()3.1 Visualization of model fit
To illustrate model behavior under different data conditions, predicted tracks were visualized for a small number of representative individuals.
# Individual with the minimum number of observations required for SSM fitting
three_obs_id <- "132071"
plot(
ssm_valid |> dplyr::filter(id == three_obs_id),
what = "predicted",
type = 1
)## $`132071`## Warning: `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## $`132071`## Warning: `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
Individuals with extremely sparse observations showed high positional uncertainty and were not used for behavioural interpretation.
# Individual with one of the largest temporal gaps between observations
large_gap_id <- "112557"
plot(
ssm_valid |> dplyr::filter(id == large_gap_id),
what = "predicted",
type = 1
)## $`112557`## Warning: `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## $`112557`## Warning: `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## # A tibble: 167 × 6
## id lat lon date lc sat
## <chr> <dbl> <dbl> <dttm> <chr> <chr>
## 1 112557 5.01 -86.2 2012-12-07 01:26:12 B NL
## 2 112557 5.05 -86.3 2012-12-07 16:07:17 B MA
## 3 112557 5.10 -86.2 2012-12-08 15:41:49 B MA
## 4 112557 5.07 -86.2 2012-12-08 18:02:57 0 NP
## 5 112557 5.26 -86.1 2012-12-08 20:20:05 0 NN
## 6 112557 5.32 -86.1 2012-12-08 22:45:34 B NK
## 7 112557 5.40 -86.0 2012-12-09 15:14:03 0 MA
## 8 112557 5.39 -86.0 2012-12-09 15:15:59 1 NL
## 9 112557 5.24 -86.1 2012-12-09 16:58:47 0 MA
## 10 112557 5.27 -86.0 2012-12-09 22:20:06 B NK
## # ℹ 157 more rowsFor this shark (id =112557), the shark has only 54 observations in 2012, with a gap of almost one year, followed by the observation almost one year, where the one year in between have huge uncertainties according to the graph.
# Individual with a more typical observation pattern
typical_id <- "164968"
plot(
ssm_valid |> dplyr::filter(id == typical_id),
what = "predicted",
type = 1
)## $`164968`## Warning: `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## $`164968`## Warning: `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
This individual shows a more typical observation pattern, with stable reconstructed tracks and moderate uncertainty.
# Typical
ty_id <- "203645"
plot(
ssm_valid |> dplyr::filter(id == ty_id),
what = "predicted",
type = 1
)## $`203645`## Warning: `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## $`203645`## Warning: `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
Visualization shark track on a spatial shapefile:
# Visualize predicted track for a representative individual
aniMotum::map(
ssm_valid |> dplyr::filter(id == "164968"),
what = "predicted"
)## using map scale: 10
# Compared with initial raw data
raw_164968 <- ggplot() +
theme_bw() +
geom_point(
data = sharks %>% dplyr::filter(id == "164968"),
aes(x = lon, y = lat)
)
print(raw_164968)
All 57 shark tracks were visualized on a spatial shapefile:
# Visualize predicted tracks for all converged individuals
aniMotum::map(
ssm_valid,
what = "predicted"
)## using map scale: 10
4 SSM diagnostics
The diagnostics are applied to the above three sharks, with 1. time series plot 2. QQ plot 3. ACF
# SSM diagnostics for representative individuals
# - sparse observations
# - large temporal gaps
# - typical observation pattern
diagnostic_ids <- c("132071", "112557", "164968")
ssm_diag <- ssm_valid |>
dplyr::filter(id %in% diagnostic_ids)
# OSAR (one step ahead residuals)
res_diag <- osar(ssm_diag)
# Time series residuals
plot(
res_diag,
type = "ts",
pages = 1
)## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at 1.4414e+09## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 31812## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 4.4986e+06## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at 1.4414e+09## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 31812## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 4.4986e+06
## Warning: `label` cannot be a <ggplot2::element_blank> object.## Warning: `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
Overall, the diagnostic plots do not raise major concerns about model fit. Residuals show no clear trends over time, their distribution is broadly consistent with model assumptions, and there is little remaining autocorrelation. This suggests the fitted state-space model adequately captures the movement dynamics in the data.
Note: Since 175953 and 203646_b failed to converge in MPM in later steps, their diagnostics are checked
# Additional SSM diagnostics for individuals that later failed MPM convergence
diagnostic_ids_MPM_failed <- c("175953", "203646_b")
ssm_diag_MPM_failed <- ssm_valid |>
dplyr::filter(id %in% diagnostic_ids_MPM_failed)
# OSAR (One-step-ahead residuals)
res_diag_MPM_failed <- osar(ssm_diag_MPM_failed)
# Time series residuals
plot(
res_diag_MPM_failed,
type = "ts",
pages = 1
)
## Warning: `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
For the shark with id = 175953, the maximum time gap between consecutive observations is 2313.52 hours. Despite this long gap, the SSM diagnostics do not show clear violations of model assumptions. The residuals are generally centered around zero without strong temporal trends, the QQ plots show only mild tail deviations, and the ACF plots for both x and y mostly fall within the confidence bounds, indicating that temporal dependence is adequately captured by the CRW model.
For the shark with id = 203646_b, the SSM diagnostics for this individual do not show major violations of model assumptions. Residuals are centred around zero with no strong temporal trends, their distribution broadly follows model expectations, and there is little remaining autocorrelation in either spatial dimension. These results suggest that the CRW-based state-space model provides an adequate description of the movement process for this track.
5 MPM (Move Persistence Model)
# Prepare input data for MPM
# Retain individuals with at least 20 predicted locations
pmm_data <- sharks_predicted %>%
dplyr::group_by(id) %>%
dplyr::filter(dplyr::n() >= 20) %>%
dplyr::ungroup()
# Fit move persistence model
pmm_fit <- fit_mpm(
pmm_data,
model = "mpm",
control = mpm_control(verbose = 0)
)## Warning in sqrt(diag(object$cov.fixed)): NaNs produced## Warning in sqrt(as.numeric(object$diag.cov.random)): NaNs produced## Warning in sqrt(diag(object$cov.fixed)): NaNs produced##
## Error in nlminb(obj$par, ifelse(control$verbose == 1, myfn, obj$fn), obj$gr, :
## NA/NaN gradient evaluation## Warning in sqrt(diag(object$cov.fixed)): NaNs produced##
##
##
##
## Error in nlminb(obj$par, ifelse(control$verbose == 1, myfn, obj$fn), obj$gr, :
## NA/NaN gradient evaluation## Warning: `label` cannot be a <ggplot2::element_blank> object.## Warning: `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.## Warning: Removed 68 rows containing missing values or values outside the scale range
## (`geom_ribbon()`).## Warning: `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## `label` cannot be a <ggplot2::element_blank> object.
## # A tibble: 33 × 4
## id mpm converged model
## <chr> <named list> <lgl> <chr>
## 1 112557 <mpm [8]> TRUE mpm
## 2 131986 <mpm [8]> TRUE mpm
## 3 132074 <mpm [8]> TRUE mpm
## 4 139119 <mpm [8]> TRUE mpm
## 5 139121 <mpm [8]> TRUE mpm
## 6 139124 <mpm [8]> TRUE mpm
## 7 139125 <mpm [8]> TRUE mpm
## 8 139127 <mpm [8]> TRUE mpm
## 9 151677 <mpm [8]> TRUE mpm
## 10 157790_a <mpm [8]> TRUE mpm
## # ℹ 23 more rowsAfter excluding individuals with fewer than 20 predicted locations, 33 sharks were retained for MPM fitting. Among these, the model did not converge for two individuals (175953 and 203646_b), which were excluded from subsequent analyses.
6 Data Extraction and preparation
# Extract fitted move persistence estimates
mpm_gamma <- grab(pmm_fit, what = "fitted") %>%
as_tibble()
# Check structure
mpm_gamma %>% glimpse()## Rows: 3,568
## Columns: 5
## $ id <chr> "112557", "112557", "112557", "112557", "112557", "112557",…
## $ date <dttm> 2012-12-07 01:00:00, 2012-12-08 01:00:00, 2012-12-09 01:00…
## $ logit_g <dbl> 2.8361115, 2.8361115, 2.8361115, 1.9693592, -2.0727940, 3.0…
## $ logit_g.se <dbl> 5.8625925, 4.5908193, 2.7894898, 1.1587468, 1.0118099, 1.16…
## $ g <dbl> 0.94459631, 0.94459631, 0.94459631, 0.87754226, 0.11176936,…# Combine latent locations with movement persistence
latent_movement <- pmm_data %>%
select(
id, date, lon, lat,
x, y, x.se, y.se
) %>%
left_join(
mpm_gamma %>% select(id, date, g),
by = c("id", "date")
)
# Sanity check: missing movement persistence values
latent_movement %>%
summarise(
n_total = n(),
n_missing_gamma = sum(is.na(g))
)## # A tibble: 1 × 2
## n_total n_missing_gamma
## <int> <int>
## 1 3739 1717 Mapping and exploratory visualization
# Time series of movement persistence (gamma_t) by individual
ggplot(latent_movement, aes(x = date, y = g)) +
geom_line(alpha = 0.6) +
facet_wrap(~ id, scales = "free_x") +
theme_bw() +
labs(
x = "Date",
y = expression(gamma[t])
)
# Spatial visualization of tracks colored by movement persistence
# Load base map
world <- rnaturalearth::ne_countries(
scale = "medium",
returnclass = "sf"
)
# Projection
prj <- "+proj=laea +lat_0=0 +lon_0=0 +datum=WGS84 +units=m +no_defs"
ggplot() +
theme_bw() +
geom_sf(data = world, fill = "grey90", colour = "grey70") +
geom_sf(
data = latent_sf,
aes(colour = g),
size = 0.7,
alpha = 0.9
) +
scale_colour_viridis_c(
name = expression(gamma[t]),
limits = c(0, 1)
) +
coord_sf(crs = prj) +
facet_wrap(~ id)
# Exploratory labeling of movement persistence values (used for visualization only; not treated as discrete states)
latent_movement <- latent_movement %>%
mutate(
behaviour_class = case_when(
g < 0.3 ~ "low_persistence",
g > 0.7 ~ "high_persistence",
TRUE ~ "intermediate"
)
)
latent_movement %>%
count(behaviour_class)## # A tibble: 3 × 2
## behaviour_class n
## <chr> <int>
## 1 high_persistence 2986
## 2 intermediate 650
## 3 low_persistence 103# Retain individuals with at least one valid persistence estimate
latent_valid <- latent_movement %>%
group_by(id) %>%
filter(any(!is.na(g))) %>%
ungroup()
# Descriptive summaries of movement persistence by individual
behaviour_summary <- latent_valid %>%
group_by(id) %>%
summarise(
n_points = n(),
mean_g = mean(g, na.rm = TRUE),
sd_g = sd(g, na.rm = TRUE),
range_g = max(g, na.rm = TRUE) - min(g, na.rm = TRUE),
lon_range = max(lon) - min(lon),
lat_range = max(lat) - min(lat)
) %>%
ungroup()
# Identify candidates with relatively typical movement persistence (used to select representative individuals for visualization)
typical_candidates <- behaviour_summary %>%
filter(
mean_g > quantile(mean_g, 0.4, na.rm = TRUE),
mean_g < quantile(mean_g, 0.6, na.rm = TRUE),
sd_g < quantile(sd_g, 0.5, na.rm = TRUE)
) %>%
arrange(sd_g)
typical_candidates## # A tibble: 2 × 7
## id n_points mean_g sd_g range_g lon_range lat_range
## <chr> <int> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 184025 22 0.873 0.00159 0.00579 3.67 4.56
## 2 220361 59 0.849 0.105 0.362 12.7 4.53Let \(\gamma_{it} \in (0,1)\) denote the movement persistence index estimated by the move persistence model for individual \(i\) at time \(t\). To summarise individual-level movement behaviour over the tracking period, we computed the following descriptive statistics of \(\gamma_{it}\).
\[ \operatorname{mean}_i(\gamma_t) \]
denoted as in the analysis, represents the average level of movement persistence for individual \(i\) across time. Values of \(\operatorname{mean}_i(\gamma_t)\) close to \(1\) indicate that the individual predominantly exhibits highly persistent, directional movement, consistent with migration-like behaviour. Values around \(0.5\) reflect intermediate persistence, suggesting mixed movement strategies. Lower values of \(\operatorname{mean}_i(\gamma_t)\) indicate movement dominated by low persistence, characterized by slower and less directed motion.
\[ \operatorname{sd}_i(\gamma_t) \]
denoted as , quantifies the temporal variability of movement persistence for individual \(i\). Low values of \(\operatorname{sd}_i(\gamma_t)\) indicate relatively stable movement behaviour over time, whereas higher values reflect substantial fluctuations in persistence, corresponding to frequent transitions between more and less directed movement.
\[ \operatorname{range}_i(\gamma_t) = \max_t(\gamma_{it}) - \min_t(\gamma_{it}) \]
denoted as , captures the extent of behavioural contrast experienced by individual \(i\) during the observation period. A small range suggests a relatively homogeneous movement pattern, while a large range indicates that the individual experienced both highly persistent and weakly persistent movement phases.
Together, these statistics characterize individual movement behaviour in terms of its average persistence, temporal stability, and behavioural heterogeneity. They are used solely for descriptive interpretation and visualization, and do not imply discrete behavioural states. All behavioural groupings based on these summaries are intended to aid interpretation of the continuous movement persistence process estimated by the model.
# High persistence candidates (for visualization)
high_persistence_candidates <- behaviour_summary %>%
filter(
mean_g > quantile(mean_g, 0.75, na.rm = TRUE),
sd_g < quantile(sd_g, 0.5, na.rm = TRUE)
) %>%
mutate(
spatial_extent = lon_range + lat_range
) %>%
arrange(desc(spatial_extent))
high_persistence_candidates## # A tibble: 7 × 8
## id n_points mean_g sd_g range_g lon_range lat_range spatial_extent
## <chr> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 157790_a 255 0.928 0.0775 4.21e-1 35.9 14.3 50.2
## 2 139119 144 1.000 0 0 12.8 10.8 23.6
## 3 139127 120 0.951 0.134 7.12e-1 8.66 8.12 16.8
## 4 139121 81 1.000 0 0 12.2 2.67 14.9
## 5 172245 70 0.998 0.00000290 7.55e-6 3.44 11.3 14.7
## 6 172239 23 0.941 0.128 5.68e-1 12.6 1.68 14.3
## 7 172240 21 0.946 0.00195 5.96e-3 8.61 1.84 10.5#Low persistence candidates (for visualization)
low_persistence_candidates <- behaviour_summary %>%
filter(
mean_g < quantile(mean_g, 0.25, na.rm = TRUE)
) %>%
arrange(sd_g)
low_persistence_candidates## # A tibble: 8 × 7
## id n_points mean_g sd_g range_g lon_range lat_range
## <chr> <int> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 184029 67 0.737 0.000205 0.000734 10.8 4.41
## 2 184027 259 0.784 0.139 0.741 24.8 10.7
## 3 132074 137 0.766 0.190 0.848 17.6 13.1
## 4 212419 67 0.683 0.198 0.631 9.41 4.35
## 5 203645 134 0.756 0.213 0.849 38.9 15.6
## 6 220362 58 0.566 0.240 0.789 11.6 4.66
## 7 139125 141 0.752 0.286 0.970 23.4 4.70
## 8 220359 31 0.670 0.393 0.941 5.21 3.79# Highly variable persistence candidates
variable_persistence_candidates <- behaviour_summary %>%
filter(
sd_g > quantile(sd_g, 0.75, na.rm = TRUE)
) %>%
arrange(desc(sd_g))
variable_persistence_candidates## # A tibble: 8 × 7
## id n_points mean_g sd_g range_g lon_range lat_range
## <chr> <int> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 220359 31 0.670 0.393 0.941 5.21 3.79
## 2 139125 141 0.752 0.286 0.970 23.4 4.70
## 3 172241 105 0.791 0.275 0.963 9.16 5.03
## 4 220362 58 0.566 0.240 0.789 11.6 4.66
## 5 203645 134 0.756 0.213 0.849 38.9 15.6
## 6 131986 70 0.793 0.211 0.741 20.8 5.08
## 7 220364 74 0.793 0.209 0.829 24.0 18.2
## 8 212419 67 0.683 0.198 0.631 9.41 4.35Here, n_points represents the number of regularized latent track points used by the move persistence model.
list(
typical = typical_candidates$id,
high_persist = high_persistence_candidates$id,
low_persist = low_persistence_candidates$id,
variable = variable_persistence_candidates$id
)## $typical
## [1] "184025" "220361"
##
## $high_persist
## [1] "157790_a" "139119" "139127" "139121" "172245" "172239" "172240"
##
## $low_persist
## [1] "184029" "184027" "132074" "212419" "203645" "220362" "139125" "220359"
##
## $variable
## [1] "220359" "139125" "172241" "220362" "203645" "131986" "220364" "212419"# Representative individuals selected for visualization
# (illustrating different persistence patterns)
rep_ids <- c(
"184025", # typical
"139119", # high persistence
"184029", # low persistence
"220359" # variable
)
latent_rep <- latent_movement %>%
dplyr::filter(id %in% rep_ids)
id_labels <- tibble(
id = rep_ids,
behaviour = c(
"Typical",
"High persistence",
"Low persistence",
"Highly variable"
)
)
latent_rep <- latent_rep %>%
left_join(id_labels, by = "id") %>%
mutate(
behaviour = factor(
behaviour,
levels = c(
"Typical",
"High persistence",
"Low persistence",
"Highly variable"
)
)
)
# Transform to sf (WGS84)
latent_rep_sf <- latent_rep %>%
sf::st_as_sf(coords = c("lon", "lat")) %>%
sf::st_set_crs(4326)
# Projection
prj <- "+proj=laea +lat_0=0 +lon_0=-90 +datum=WGS84 +units=m +no_defs"
latent_rep_proj <- latent_rep_sf %>%
sf::st_transform(crs = prj)
# In meters
bbox_proj <- sf::st_bbox(latent_rep_proj)
x_buffer <- 5e5 # 500 km buffer
y_buffer <- 5e5
xlim_zoom <- c(
bbox_proj["xmin"] - x_buffer,
bbox_proj["xmax"] + x_buffer
)
ylim_zoom <- c(
bbox_proj["ymin"] - y_buffer,
bbox_proj["ymax"] + y_buffer
)
world <- rnaturalearth::ne_countries(
scale = "medium",
returnclass = "sf"
)
world_proj <- world %>%
sf::st_transform(crs = prj)
ggplot() +
theme_bw() +
geom_sf(
data = world_proj,
fill = "grey90",
colour = "grey70",
linewidth = 0.2
) +
geom_sf(
data = latent_rep_proj,
aes(colour = g),
size = 1,
alpha = 0.9
) +
scale_colour_viridis_c(
name = expression(gamma[t]),
limits = c(0, 1)
) +
coord_sf(
crs = prj,
xlim = xlim_zoom,
ylim = ylim_zoom,
expand = FALSE
) +
facet_wrap(~ behaviour + id, ncol = 2)
The overview map uses a shared spatial scale across individuals, which facilitates comparison of movement extent but compresses trajectories with smaller spatial ranges. To highlight individual-level movement geometry, there are additionally maps zoomed to the spatial extent of each track.
# Zoom in map
plot_one_shark_map <- function(
latent_data,
shark_id,
behaviour_label,
prj,
buffer_km = 300
) {
# subset one individual
df_one <- latent_data %>%
dplyr::filter(id == shark_id)
# convert to sf (lon/lat)
sf_one <- df_one %>%
sf::st_as_sf(coords = c("lon", "lat")) %>%
sf::st_set_crs(4326) %>%
sf::st_transform(crs = prj)
# bounding box in projected CRS (meters)
bb <- sf::st_bbox(sf_one)
buffer_m <- buffer_km * 1000
xlim <- c(bb["xmin"] - buffer_m, bb["xmax"] + buffer_m)
ylim <- c(bb["ymin"] - buffer_m, bb["ymax"] + buffer_m)
# world map
world_proj <- rnaturalearth::ne_countries(
scale = "medium",
returnclass = "sf"
) %>%
sf::st_transform(crs = prj)
# plot
ggplot() +
theme_bw() +
geom_sf(
data = world_proj,
fill = "grey90",
colour = "grey70",
linewidth = 0.2
) +
geom_sf(
data = sf_one,
aes(colour = g),
size = 1.2
) +
scale_colour_viridis_c(
name = expression(gamma[t]),
limits = c(0, 1)
) +
coord_sf(
crs = prj,
xlim = xlim,
ylim = ylim,
expand = FALSE
) +
labs(
title = behaviour_label,
subtitle = paste("ID:", shark_id)
)
}
prj <- "+proj=laea +lat_0=0 +lon_0=-90 +datum=WGS84 +units=m +no_defs"
# Typical
plot_one_shark_map(
latent_data = latent_movement,
shark_id = "184025",
behaviour_label = "Typical",
prj = prj,
buffer_km = 300
)
# High persistence
plot_one_shark_map(
latent_data = latent_movement,
shark_id = "139119",
behaviour_label = "High persistence",
prj = prj,
buffer_km = 500
)
# Low persistence
plot_one_shark_map(
latent_data = latent_movement,
shark_id = "184029",
behaviour_label = "Low persistence",
prj = prj,
buffer_km = 200
)
# Highly variable
plot_one_shark_map(
latent_data = latent_movement,
shark_id = "220359",
behaviour_label = "Highly variable",
prj = prj,
buffer_km = 200
)
# Check
plot_one_shark_map(
latent_data = latent_movement,
shark_id = "172246",
behaviour_label = "/",
prj = prj,
buffer_km = 500
)## Warning in min(cc[[1]], na.rm = TRUE): no non-missing arguments to min;
## returning Inf## Warning in min(cc[[2]], na.rm = TRUE): no non-missing arguments to min;
## returning Inf## Warning in max(cc[[1]], na.rm = TRUE): no non-missing arguments to max;
## returning -Inf## Warning in max(cc[[2]], na.rm = TRUE): no non-missing arguments to max;
## returning -Inf